New York (CNN) -- The federal courts face an unprecedented challenge in trying accused 9/11 mastermind Khalid Sheikh Mohammed and four other Guantanamo detainees for the terrorist attacks that took 3,000 lives, says CNN legal analyst Jeffrey Toobin.

Mohammed, Ramzi Bin al-Shibh, Walid bin Attash, Ali Abdul Aziz Ali and Mustafa Ahmed al-Hawsawi and four other Guantanamo detainees are being transferred to New York to face trial in a civilian court for the September 11 attacks, Attorney General Eric Holder announced Friday.

They will face trial in the U.S. District Court for the Southern District of New York -- a short distance from the World Trade Center towers that were destroyed in the September 11 attacks. Holder said he expects the government to seek the death penalty in the cases.

Mohammed is the confessed organizer of the attacks on New York and the Pentagon. But his confession could be called into question during trial. A 2005 Justice Department memo -- released by the Obama administration -- revealed he had been waterboarded 183 times in March 2003, a technique that President Obama has called torture.

CNN spoke with Toobin on Friday morning. A former assistant U.S. attorney, Toobin is a senior analyst for CNN and author of "The Nine: Inside the Secret World of the Supreme Court."

CNN: What's the significance of today's announcement that Khalid Sheikh Mohammed will be tried in federal court?

Toobin: It's perhaps the biggest challenge in the history of federal law enforcement to produce a trial that is fair under these circumstances.

CNN: What are the parallels to this case?

Toobin: The closest is the trial of Omar Abdel Rahman, the blind sheikh who was tried in the same courthouse in connection with the World Trade Center attack of 1993. But as we all know, the scale of 9/11 is vastly greater

CNN: What are the obstacles to a fair trial?

Toobin: Just for example, how do they deal with the fact that Khalid Sheikh Mohammed was extensively tortured? The defense will argue that 183 waterboardings is misconduct that means the whole case should be thrown out.

If the case isn't thrown out, how do you deal with the statements he made after the interrogations or the leads that were generated after that?

How do you pick a jury in a courthouse just a few blocks away from the World Trade Center site that can be considered fair? Can you have a change of venue? ... And the biggest issue of all is what happens if he's acquitted? Can anyone envision a scenario where Khalid Sheikh Mohammed walks down the courthouse steps?

CNN: If this were an ordinary case, how would the use of coercive interrogation techniques affect the outcome?

Toobin: I have no doubt that statements made under that kind of torture would not be admitted in a federal court. The question is whether the whole case would be thrown out. I don't think this case will be thrown out.

The chronology of his statements to the authorities is going to be a very key issue. Even if he made voluntary statements after the waterboardings, even months later, they could be tainted.

CNN: How will Mohammed be defended in court?

Toobin: Since this is a death penalty case, he will have an extensive defense team paid for by the federal government.

CNN: How long will it be before the case comes to trial?

Toobin: At least a year, maybe two before it comes to trial. You have to have security in place, you're going to have to set up a system where victims and families will have access to watching. In the Oklahoma City bombing case, there was a separate courtroom with a video feed for 165 victims' families. You're talking about 3,000 victims here. The issue of access to classified information -- the defense is entitled to see the evidence against him, some of which is classified. Are they going to allow Mohammed to see classified evidence? Then the question of what evidence can be used, the question of change of venue, can an unbiased jury be found in New York?

CNN: Will Khalid Sheikh Mohammed be seen as a proxy for Osama bin Laden?

Toobin: I think our judicial system tries not to work that way. We try one defendant at a time for one set of facts and one set of charges, and that's as it should be.